Abstract
The extraction of information from texts requires resources that contain both syntactic and semantic properties of lexical units. As the use of language in specialized domains, such as biology, can be very different to the general domain, there is a need for domain-specific resources to ensure that the information extracted is as accurate as possible. We are building a large-scale lexical resource for the biology domain, providing information about predicate-argument structure that has been bootstrapped from a biomedical corpus on the subject of E. Coli. The lexicon is currently focussed on verbs, and includes both automatically-extracted syntactic subcategorization frames, as well as semantic event frames that are based on annotation by domain experts. In addition, the lexicon contains manually-added explicit links between semantic and syntactic slots in corresponding frames. To our knowledge, this lexicon currently represents a unique resource within in the biomedical domain.
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References
Rebholz-Schuhmann, D., Pezik, P., Lee, V., Kim, J.-J., del Gratta, R., Sasaki, Y., McNaught, J., Montemagni, S., Monachini, M., Calzolari, N., Ananiadou, S.: BioLexicon: Towards a Reference Terminological Resource in the Biomedical Domain. In: Proc. of 16th Ann. Int. Conf. on Intelligent Systems for Molecular Biology (ISMB 2008), Toronto, Canada (2008)
Ruppenhofer, J., Ellsworth, M., Petruck, M., Johnson, C., Scheffczyk, J.: FrameNet II: Extended Theory and Practice (2006), http://framenet.icsi.berkeley.edu/
Palmer, M., Kingsbury, P., Gildea, D.: The Proposition Bank: An Annotated Corpus of Semantic Roles. Computational Linguistics 31(1), 71–106 (2005)
Fillmore, C.J.: Frame semantics and the nature of language. In: Annals of the New York Academy of Sciences: Conference on the Origin and Development of Language and Speech, vol. 280, pp. 20–32 (1976)
Dolbey, A., Ellsworth, M., Scheffczykx, J.: BioFrameNet: A Domain-Specific FrameNet Extension with Links to Biomedical Ontologies. In: Bodenreider, O. (ed.) Proceedings of KR-MED, pp. 87–94 (2006)
Wattarujeekrit, T., Shah, P., Collier, N.: PASBio: predicate-argument structures for event extraction in molecular biology. BMC Bioinformatics 5(155) (2004)
Browne, A.C., Divita, G., Aronson, A.R., McCray, A.T.: UMLS Language and Vocabulary Tools. In: Proceedings of AMIA Annual Symposium, p. 798 (2003)
Tsai, R.T.H., Chou, W.C., Su, Y.S., Lin, Y.C., Sung, C.L., Dai, H.J., Yeh, I.T.H., Ku, W., Sung, T.Y., Hsu, W.L.: BIOSMILE: A semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features. BMC Bioinformatics 8(325) (2006)
Miyao, Y., Ninomiya, T., Tsujii, J.: Corpus-oriented grammar development for acquiring a head-driven phrase structure grammar from the penn treebank. In: Su, K.-Y., Tsujii, J., Lee, J.-H., Kwong, O.Y. (eds.) IJCNLP 2004. LNCS, vol. 3248, pp. 684–693. Springer, Heidelberg (2005)
Hara, T., Miyao, Y., Tsujii, J.: Adapting a probabilistic disambiguation model of an HPSG parser to a new domain. In: Dale, R., Wong, K.-F., Su, J., Kwong, O.Y. (eds.) IJCNLP 2005. LNCS, vol. 3651, pp. 199–210. Springer, Heidelberg (2005)
Thompson, P., Cotter, P., Ananiadou, S., McNaught, J., Montemagni, S., Trabucco, A., Venturi, G.: Building a Bio-Event Annotated Corpus for the Acquisition of Semantic Frames from Biomedical Corpora. In: Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC 2008) (2008)
Kipper-Schuler, K.: VerbNet: A broad-coverage, comprehensive verb lexicon. PhD. Thesis. Computer and Information Science Dept., University of Pennsylvania, Philadelphia, PA (2005)
Lenci, A., Busa, F., Ruimy, N., Gola, E., Monachini, M., Calzolari, N., Zampolli, A., et al.: SIMPLE Linguistic Specifications LE-SIMPLE (LE4-8346), Deliverable D2.1 & D2.2. ILC and University of Pisa (2000)
Montemagni, S., Trabucco, A., Venturi, G., Thompson, P., Cotter, P., Ananiadou, S., McNaught, J., Kim, J.-J., Rebholz-Schuhmann, D., Pezik, P.: Event annotation of domain corpora, BOOTStrep (FP6 – 028099), Deliverable 4.1. University of Manchester, ILC-CNR and European Bioinformatics Institute (2007)
Fillmore, C.J.: The case for case. In: Bach, E., Harms, R.T. (eds.) Universals in Linguistic Theory, pp. 1–88. Holt, Rinehart, and Winston, New York (1968)
Levin, B., Rappaport Hovav, M.: Lexical Semantics and Syntactic Structure. In: Lappin, S. (ed.) The Handbook of Contemporary Semantic Theory, pp. 487–507. Blackwell, Oxford (1996)
Cohen, K.B., Hunter, L.: A critical review of PASBio’s argument structures for biomedical verbs. BMC Bioinformatics 7(Suppl. 3), S5 (2006)
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Venturi, G. et al. (2009). Bootstrapping a Verb Lexicon for Biomedical Information Extraction. In: Gelbukh, A. (eds) Computational Linguistics and Intelligent Text Processing. CICLing 2009. Lecture Notes in Computer Science, vol 5449. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-00382-0_11
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